The genetic organization of the HLA complex was analyzed by studying genomic DNA restriction enzyme polymorphisms in eight fmailies that were known to include individuals inheriting recombinant HLA haplotypes. Cloned DNA corresponding to class I, class II (DRAlpha, DRBeta, DCAlpha, DCBeta and SBBeta) and class III (C4) major histocompatibility complex genes were used as probes in Southern blotting analysis. Polymorphism in the size of restriction fragments from the various major histocompatibility genes were observed with certain enzymes and could be assigned to haplotypes in families. The results to date have made it possible to: (l) identify a previously undetected crossover event in one family; (2) to localize the gene encoding C4 within the HLA complex between HLA-B and HLA-DR; (3) to distinguish HLSA-DR-DC-SB haplotypes that type identically and, (4) to more precisely define the location of the crossover event in each recombinant haplotype.